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- PDB-2vzw: X-ray structure of the heme-bound GAF domain of sensory histidine... -

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Basic information

Entry
Database: PDB / ID: 2vzw
TitleX-ray structure of the heme-bound GAF domain of sensory histidine kinase DosT of Mycobacterium tuberculosis
ComponentsPROBABLE HISTIDINE KINASE RESPONSE REGULATOR
KeywordsTRANSFERASE / OXYGEN BINDING / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


detection of hypoxia / protein histidine kinase activity / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / histidine kinase / phosphorelay sensor kinase activity / oxygen binding / protein autophosphorylation / membrane => GO:0016020 ...detection of hypoxia / protein histidine kinase activity / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / histidine kinase / phosphorelay sensor kinase activity / oxygen binding / protein autophosphorylation / membrane => GO:0016020 / protein dimerization activity / protein kinase activity / calcium ion binding / heme binding / magnesium ion binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
GAF domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / GAF domain / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...GAF domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / GAF domain / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Oxygen sensor histidine kinase response regulator DosT / Oxygen sensor histidine kinase response regulator DosT
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPodust, L.M. / Ioanoviciu, A. / Ortiz de Montellano, P.R.
CitationJournal: Biochemistry / Year: 2008
Title: 2.3 A X-Ray Structure of the Heme-Bound Gaf Domain of Sensory Histidine Kinase Dost of Mycobacterium Tuberculosis.
Authors: Podust, L.M. / Ioanoviciu, A. / Ortiz de Montellano, P.R.
History
DepositionAug 6, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 6, 2013Group: Data collection
Revision 1.3Feb 7, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Mar 11, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE HISTIDINE KINASE RESPONSE REGULATOR
B: PROBABLE HISTIDINE KINASE RESPONSE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0987
Polymers32,7152
Non-polymers1,3835
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-63 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.924, 87.924, 66.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PROBABLE HISTIDINE KINASE RESPONSE REGULATOR / GAF FAMILY PROTEIN / DOST


Mass: 16357.447 Da / Num. of mol.: 2 / Fragment: GAF SENSORY DOMAIN, RESIDUES 61-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Gene: RV2027C / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53473, UniProt: P9WGK1*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsOXYGEN (OXY): COORDINATION BOND TO THE HEME IRON PROTOPORPHYRIN IX CONTAINING FE (HEM): ...OXYGEN (OXY): COORDINATION BOND TO THE HEME IRON PROTOPORPHYRIN IX CONTAINING FE (HEM): COORDINATION BOND BETWEEN FE AND HIS 147
Sequence detailsENGINEERED FIRST RESIDUE GLY 60

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.6 % / Description: NONE
Crystal growpH: 6 / Details: 50% TACSIMATE, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587, 1.73989, 1.65312
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 29, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.739891
31.653121
ReflectionResolution: 2.3→50 Å / Num. obs: 22939 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 47
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
ELVESphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→88.05 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 16.5 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 1171 5.1 %RANDOM
Rwork0.23634 ---
obs0.23908 21731 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→88.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 96 109 2467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222467
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2882.0833388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8755303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98222.632114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.56915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4841526
X-RAY DIFFRACTIONr_chiral_restr0.1470.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021962
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.21222
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21653
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.51544
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42922401
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4931043
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6774.5983
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.296→2.355 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 87
Rwork0.256 1605
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8502-0.93780.42284.92811.62441.759-0.0160.07870.20660.0257-0.0053-0.0759-0.1576-0.07770.0213-0.14520.0284-0.0453-0.1881-0.0366-0.0673-11.97217.24660.224
23.6014-0.1754-1.59433.6494-0.02052.8262-0.1454-0.057-0.02940.10730.1422-0.09930.08710.28640.0031-0.22740.03330.0043-0.15820.0153-0.0678-27.89730.91679.298
311.2038-2.6864-1.32468.37195.79834.04360.04410.79990.9072-0.41470.3117-0.03840.3894-0.2691-0.3558-0.11480.0204-0.0524-0.0504-0.00120.1619-10.2939.44856.34
414.9922-8.8503-4.33975.48693.44824.252-0.6879-0.3545-0.05980.5980.13720.73840.04760.13610.5507-0.12410.05430.1598-0.13540.16630.0886-35.19833.21684.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 205
2X-RAY DIFFRACTION2B60 - 208
3X-RAY DIFFRACTION3A1206
4X-RAY DIFFRACTION4B1209

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